Présentation de l’application de colSBM sur Doré et al. 2020
Clustering avec le modèle iid
Avec le modèle iid nous obtenons les 5 collections suivantes:
| collection_id | net_id |
|---|---|
| 1 | arroyo1982_1+arroyo1982_2+arroyo3 |
| 1 | eberling1999 |
| 1 | kato1990 |
| 1 | petanidou1991 |
| 1 | Junker2013 |
| 1 | bartomeus2008 |
| 1 | Benadi2013_1(950m)+Benadi2013_2(1170m)+Benadi2013_6(2020m) |
| 1 | Benadi2013_4(1700m)+Benadi2013_5(1800m) |
| 1 | Struck1994 |
| 1 | Kato2000 |
| 1 | Albrecht2010_49yr+Albrecht2010_63yr+Albrecht2010_84yr+Albrecht2010_109yr+Albrecht2010_130yr |
| 1 | Baldock2011_TB+Baldock2011_JN |
| 1 | Dattilo2016 |
| 1 | Devoto2005_PP+Devoto2005_AP |
| 1 | Devoto2005_VT |
| 1 | Devoto2005_LL+Devoto2005_CT |
| 1 | Freitas2006 |
| 1 | Gibson2006_TA2 |
| 1 | Jedrzejewska2013_Ochata+Jedrzejewska2013_Kabaty |
| 1 | MonteroCastano2017_Albufera+MonteroCastano2017_Llimpa+MonteroCastano2017_Tirant |
| 1 | Kehinde2014_Joostenberg_Conv+Kehinde2014_Joostenberg_Org+Kehinde2014_Joostenberg_Nat+Kehinde2014_Laibach_Conv+Kehinde2014_Laibach_Org+Kehinde2014_Laibach_Nat+Kehinde2014_Spier_Conv+Kehinde2014_Spier_Nat |
| 1 | Pinheiro2008 |
| 1 | Watts2016_Chicon+Watts2016_Mantanay+Watts2016_Choquebamba+Watts2016_Huaran+Watts2016_Piscacucho+Watts2016_Poques+Watts2016_Pumamarca+Watts2016_Tiaparo+Watts2016_Yanacocha |
| 1 | Kato1993 |
| 1 | KatoMiura1996 |
| 1 | Kakutani1990 |
| 1 | Inoue1990 |
| 1 | Fragoso_RA2+Fragoso_RA3+Fragoso_RD1+Fragoso_RD3 |
| 1 | Souza_cerrado |
| 1 | Souza_chaco |
| 1 | Souza_pantanal |
| 1 | Souza_vereda |
| 1 | Adedoja2019 |
| 1 | Oleques2019 |
| 1 | Baldock2019_Bristol |
| 1 | Baldock2019_Edinburgh |
| 1 | Baldock2019_Leeds |
| 1 | Baldock2019_Reading |
| collection_id | net_id |
|---|---|
| 2 | dupont2003 |
| 2 | herrera1988 |
| 2 | inouye1988 |
| 2 | medan2002ld |
| 2 | medan2002rb |
| 2 | ramirez1992 |
| 2 | ramirez1989 |
| 2 | Burkle2013 |
| 2 | Olito-Fox2014 |
| 2 | Benadi2013_3(1340m) |
| 2 | Aizen2008_Challhuaco_U+Aizen2008_Challhuaco_D |
| 2 | Aizen2008_Cerro Otto_U+Aizen2008_Cerro Otto_D |
| 2 | Aizen2008_Llao-llao_U+Aizen2008_Llao-llao_D |
| 2 | Chamberlain_cr1+Chamberlain_cr2+Chamberlain_fs1+Chamberlain_fs2+Chamberlain_go1+Chamberlain_go2+Chamberlain_mm1+Chamberlain_mm2+Chamberlain_mz1+Chamberlain_mz2+Chamberlain_sm1+Chamberlain_sm2 |
| 2 | Chamberlain_HLU+Chamberlain_HLG+Chamberlain_OKU+Chamberlain_OKG+Chamberlain_WLU+Chamberlain_WLG+Chamberlain_SOU+Chamberlain_SOG |
| 2 | Devoto2005_LQ |
| 2 | Devoto2005_LT+Devoto2005_LH |
| 2 | LemusJimenez2003 |
| 2 | Lundgren2005 |
| 2 | Marrero2013 |
| 2 | Trojelsgaard2015_La Gomera |
| 2 | Trojelsgaard2015_Gran Canaria |
| 2 | Zackenberg |
| 2 | Yoshihara2008 |
| 2 | Fragoso_RA1+Fragoso_RD2 |
| 2 | PopicThesis |
| 2 | Pornon2017 |
| 2 | Orford_B1+Orford_B2+Orford_B3+Orford_B4+Orford_B5+Orford_B10 |
| 2 | Orford_B6+Orford_B7+Orford_B8+Orford_B9 |
| 2 | Blumel2016 |
| 2 | Kantsa2018 |
| 2 | Bennett2018 |
| 2 | Adedoja2018b_baseZone+Adedoja2018b_MidZone+Adedoja2018b_HighZone+Adedoja2018b_PeakZone |
| 2 | CordenizPicanco2018_NatVeg |
| 2 | CordenizPicanco2018_ExoFor |
| 2 | Benadi2018 |
| 2 | Hackett2019_NZ_salt_marsh+Hackett2019_NZ_sand_dune+Hackett2019_NZ_scrub_coprosma |
| 2 | Jolls2019 |
| 2 | Traveset2013_Fernandina |
| 2 | Traveset2013_Pinta |
| 2 | Traveset2013_Santiago |
| 2 | Traveset2013_SantaCruz |
| 2 | Traveset2013_SanCristobal |
| 2 | Simanonok2014 |
| 2 | Son2019_a1+Son2019_a2+Son2019_a3+Son2019_a4+Son2019_a5+Son2019_a6+Son2019_a7+Son2019_a8+Son2019_F1+Son2019_F2+Son2019_F3+Son2019_F4+Son2019_F5+Son2019_F6+Son2019_F7+Son2019_F8 |
| collection_id | net_id |
|---|---|
| 3 | small1976 |
| collection_id | net_id |
|---|---|
| 4 | smith-ramirez2005 |
| 4 | Weiner2011 |
| 4 | Kaiser_control+Kaiser_restored |
| 4 | Gilarranz2014_amarante+Gilarranz2014_barrosa+Gilarranz2014_cincocerros+Gilarranz2014_difuntito+Gilarranz2014_difuntos+Gilarranz2014_elmorro+Gilarranz2014_labrava+Gilarranz2014_lachata+Gilarranz2014_lapaja+Gilarranz2014_piedraalta+Gilarranz2014_vigilancia+Gilarranz2014_volcan |
| 4 | Kaiser-Bunbury2017_Bernica+Kaiser-Bunbury2017_Casse-dent+Kaiser-Bunbury2017_Copolia+Kaiser-Bunbury2017_La-Reserve+Kaiser-Bunbury2017_Rosebelle+Kaiser-Bunbury2017_Salazie+Kaiser-Bunbury2017_Tea-Plantation+Kaiser-Bunbury2017_Trois-Freres |
| 4 | Fang2012 |
| 4 | Aizen2008_Puerto Blest_U+Aizen2008_Puerto Blest_D |
| 4 | Chamberlain_Site1+Chamberlain_Site2+Chamberlain_Site3+Chamberlain_Site4+Chamberlain_Site5+Chamberlain_Site6 |
| 4 | Dupont2009_IsenBjerg+Dupont2009_Other |
| 4 | Gibson2006_GA1 |
| 4 | Gibson2006_TA1 |
| 4 | LaraRomero2016_pe?alara_EP+LaraRomero2016_pe?alara_PA+LaraRomero2016_nevero_EP+LaraRomero2016_nevero_PA |
| 4 | Trojelsgaard2015_Tenerife Teno Bajo+Trojelsgaard2015_Tenerife Fasnia |
| 4 | Vanbergen2013_balfarm+Vanbergen2013_bridgend+Vanbergen2013_dalhaikie+Vanbergen2013_netherton+Vanbergen2013_backhill+Vanbergen2013_corntulloch+Vanbergen2013_allancreich |
| 4 | Pfeiffer_CNE+Pfeiffer_CNM+Pfeiffer_CNT+Pfeiffer_CPB+Pfeiffer_CPM+Pfeiffer_CPR+Pfeiffer_CPS+Pfeiffer_M2+Pfeiffer_RP1+Pfeiffer_RP2+Pfeiffer_LM+Pfeiffer_LO+Pfeiffer_BD+Pfeiffer_BH+Pfeiffer_BS |
| 4 | Carstensen_Gigante+Carstensen_Paulino+Carstensen_Tinkerbell+Carstensen_Midway+Carstensen_Cedro+Carstensen_Elefante+Carstensen_Soizig |
| 4 | Welti_ID+Welti_K1B+Welti_K4A+Welti_4B+Welti_20B+Welti_20C+Welti_N1A+Welti_N1B+Welti_N4A+Welti_N4B+Welti_N20A+Welti_N20B |
| 4 | Grass2013_1+Grass2013_2+Grass2013_3+Grass2013_4+Grass2013_5+Grass2013_6+Grass2013_7+Grass2013_8+Grass2013_9+Grass2013_10+Grass2013_11+Grass2013_12+Grass2013_13+Grass2013_14+Grass2013_15+Grass2013_16+Grass2013_17 |
| 4 | Hackett2019_UK_sand_dune+Hackett2019_UK_grassland+Hackett2019_UK_heathland+Hackett2019_UK_woodland+Hackett2019_UK_salt_marsh+Hackett2019_UK_scrub |
| 4 | Neli2014 |
| collection_id | net_id |
|---|---|
| 5 | olensen2002aig |
| 5 | olensen2002flo |
| 5 | vazquez2002 |
| 5 | Shay2016 |
| 5 | Gibson2006_GA2 |
| 5 | Gibson2006_SG |
| 5 | Trojelsgaard2015_El Hierro |
| 5 | Trojelsgaard2015_Fuerteventura |
| 5 | Trojelsgaard2015_Western Sahara |
| 5 | Robinson2018 |
| 5 | CordenizPicanco2018_NatFor |
| 5 | CordenizPicanco2018_SemiPast |
| 5 | CordenizPicanco2018_IntPast |
| 5 | Biella2019 |
| 5 | Nel2017 |
| 5 | Villalobos2019 |
| 5 | LaraRomero2019_blanca+LaraRomero2019_rajada+LaraRomero2019_refugio+LaraRomero2019_torre |
| 5 | Ferrero2013 |
| 5 | Sritongchuay2019_near+Sritongchuay2019_far |
Une fois le modèle de collection appliqué nous obtenons les structures suivantes:
##
## Pour la collection 1 du modèle *iid*
## [1] "arroyo1982_1+arroyo1982_2+arroyo3"
## [2] "eberling1999"
## [3] "kato1990"
## [4] "petanidou1991"
## [5] "Junker2013"
## [6] "bartomeus2008"
## [7] "Benadi2013_1(950m)+Benadi2013_2(1170m)+Benadi2013_6(2020m)"
## [8] "Benadi2013_4(1700m)+Benadi2013_5(1800m)"
## [9] "Struck1994"
## [10] "Kato2000"
## [11] "Albrecht2010_49yr+Albrecht2010_63yr+Albrecht2010_84yr+Albrecht2010_109yr+Albrecht2010_130yr"
## [12] "Baldock2011_TB+Baldock2011_JN"
## [13] "Dattilo2016"
## [14] "Devoto2005_PP+Devoto2005_AP"
## [15] "Devoto2005_VT"
## [16] "Devoto2005_LL+Devoto2005_CT"
## [17] "Freitas2006"
## [18] "Gibson2006_TA2"
## [19] "Jedrzejewska2013_Ochata+Jedrzejewska2013_Kabaty"
## [20] "MonteroCastano2017_Albufera+MonteroCastano2017_Llimpa+MonteroCastano2017_Tirant"
## [21] "Kehinde2014_Joostenberg_Conv+Kehinde2014_Joostenberg_Org+Kehinde2014_Joostenberg_Nat+Kehinde2014_Laibach_Conv+Kehinde2014_Laibach_Org+Kehinde2014_Laibach_Nat+Kehinde2014_Spier_Conv+Kehinde2014_Spier_Nat"
## [22] "Pinheiro2008"
## [23] "Watts2016_Chicon+Watts2016_Mantanay+Watts2016_Choquebamba+Watts2016_Huaran+Watts2016_Piscacucho+Watts2016_Poques+Watts2016_Pumamarca+Watts2016_Tiaparo+Watts2016_Yanacocha"
## [24] "Kato1993"
## [25] "KatoMiura1996"
## [26] "Kakutani1990"
## [27] "Inoue1990"
## [28] "Fragoso_RA2+Fragoso_RA3+Fragoso_RD1+Fragoso_RD3"
## [29] "Souza_cerrado"
## [30] "Souza_chaco"
## [31] "Souza_pantanal"
## [32] "Souza_vereda"
## [33] "Adedoja2019"
## [34] "Oleques2019"
## [35] "Baldock2019_Bristol"
## [36] "Baldock2019_Edinburgh"
## [37] "Baldock2019_Leeds"
## [38] "Baldock2019_Reading"
##
## Pour la collection 2 du modèle *iid*
## [1] "dupont2003"
## [2] "herrera1988"
## [3] "inouye1988"
## [4] "medan2002ld"
## [5] "medan2002rb"
## [6] "ramirez1992"
## [7] "ramirez1989"
## [8] "Burkle2013"
## [9] "Olito-Fox2014"
## [10] "Benadi2013_3(1340m)"
## [11] "Aizen2008_Challhuaco_U+Aizen2008_Challhuaco_D"
## [12] "Aizen2008_Cerro Otto_U+Aizen2008_Cerro Otto_D"
## [13] "Aizen2008_Llao-llao_U+Aizen2008_Llao-llao_D"
## [14] "Chamberlain_cr1+Chamberlain_cr2+Chamberlain_fs1+Chamberlain_fs2+Chamberlain_go1+Chamberlain_go2+Chamberlain_mm1+Chamberlain_mm2+Chamberlain_mz1+Chamberlain_mz2+Chamberlain_sm1+Chamberlain_sm2"
## [15] "Chamberlain_HLU+Chamberlain_HLG+Chamberlain_OKU+Chamberlain_OKG+Chamberlain_WLU+Chamberlain_WLG+Chamberlain_SOU+Chamberlain_SOG"
## [16] "Devoto2005_LQ"
## [17] "Devoto2005_LT+Devoto2005_LH"
## [18] "LemusJimenez2003"
## [19] "Lundgren2005"
## [20] "Marrero2013"
## [21] "Trojelsgaard2015_La Gomera"
## [22] "Trojelsgaard2015_Gran Canaria"
## [23] "Zackenberg"
## [24] "Yoshihara2008"
## [25] "Fragoso_RA1+Fragoso_RD2"
## [26] "PopicThesis"
## [27] "Pornon2017"
## [28] "Orford_B1+Orford_B2+Orford_B3+Orford_B4+Orford_B5+Orford_B10"
## [29] "Orford_B6+Orford_B7+Orford_B8+Orford_B9"
## [30] "Blumel2016"
## [31] "Kantsa2018"
## [32] "Bennett2018"
## [33] "Adedoja2018b_baseZone+Adedoja2018b_MidZone+Adedoja2018b_HighZone+Adedoja2018b_PeakZone"
## [34] "CordenizPicanco2018_NatVeg"
## [35] "CordenizPicanco2018_ExoFor"
## [36] "Benadi2018"
## [37] "Hackett2019_NZ_salt_marsh+Hackett2019_NZ_sand_dune+Hackett2019_NZ_scrub_coprosma"
## [38] "Jolls2019"
## [39] "Traveset2013_Fernandina"
## [40] "Traveset2013_Pinta"
## [41] "Traveset2013_Santiago"
## [42] "Traveset2013_SantaCruz"
## [43] "Traveset2013_SanCristobal"
## [44] "Simanonok2014"
## [45] "Son2019_a1+Son2019_a2+Son2019_a3+Son2019_a4+Son2019_a5+Son2019_a6+Son2019_a7+Son2019_a8+Son2019_F1+Son2019_F2+Son2019_F3+Son2019_F4+Son2019_F5+Son2019_F6+Son2019_F7+Son2019_F8"
##
## Pour la collection 3 du modèle *iid*
## [1] "small1976"
##
## Pour la collection 4 du modèle *iid*
## [1] "smith-ramirez2005"
## [2] "Weiner2011"
## [3] "Kaiser_control+Kaiser_restored"
## [4] "Gilarranz2014_amarante+Gilarranz2014_barrosa+Gilarranz2014_cincocerros+Gilarranz2014_difuntito+Gilarranz2014_difuntos+Gilarranz2014_elmorro+Gilarranz2014_labrava+Gilarranz2014_lachata+Gilarranz2014_lapaja+Gilarranz2014_piedraalta+Gilarranz2014_vigilancia+Gilarranz2014_volcan"
## [5] "Kaiser-Bunbury2017_Bernica+Kaiser-Bunbury2017_Casse-dent+Kaiser-Bunbury2017_Copolia+Kaiser-Bunbury2017_La-Reserve+Kaiser-Bunbury2017_Rosebelle+Kaiser-Bunbury2017_Salazie+Kaiser-Bunbury2017_Tea-Plantation+Kaiser-Bunbury2017_Trois-Freres"
## [6] "Fang2012"
## [7] "Aizen2008_Puerto Blest_U+Aizen2008_Puerto Blest_D"
## [8] "Chamberlain_Site1+Chamberlain_Site2+Chamberlain_Site3+Chamberlain_Site4+Chamberlain_Site5+Chamberlain_Site6"
## [9] "Dupont2009_IsenBjerg+Dupont2009_Other"
## [10] "Gibson2006_GA1"
## [11] "Gibson2006_TA1"
## [12] "LaraRomero2016_pe?alara_EP+LaraRomero2016_pe?alara_PA+LaraRomero2016_nevero_EP+LaraRomero2016_nevero_PA"
## [13] "Trojelsgaard2015_Tenerife Teno Bajo+Trojelsgaard2015_Tenerife Fasnia"
## [14] "Vanbergen2013_balfarm+Vanbergen2013_bridgend+Vanbergen2013_dalhaikie+Vanbergen2013_netherton+Vanbergen2013_backhill+Vanbergen2013_corntulloch+Vanbergen2013_allancreich"
## [15] "Pfeiffer_CNE+Pfeiffer_CNM+Pfeiffer_CNT+Pfeiffer_CPB+Pfeiffer_CPM+Pfeiffer_CPR+Pfeiffer_CPS+Pfeiffer_M2+Pfeiffer_RP1+Pfeiffer_RP2+Pfeiffer_LM+Pfeiffer_LO+Pfeiffer_BD+Pfeiffer_BH+Pfeiffer_BS"
## [16] "Carstensen_Gigante+Carstensen_Paulino+Carstensen_Tinkerbell+Carstensen_Midway+Carstensen_Cedro+Carstensen_Elefante+Carstensen_Soizig"
## [17] "Welti_ID+Welti_K1B+Welti_K4A+Welti_4B+Welti_20B+Welti_20C+Welti_N1A+Welti_N1B+Welti_N4A+Welti_N4B+Welti_N20A+Welti_N20B"
## [18] "Grass2013_1+Grass2013_2+Grass2013_3+Grass2013_4+Grass2013_5+Grass2013_6+Grass2013_7+Grass2013_8+Grass2013_9+Grass2013_10+Grass2013_11+Grass2013_12+Grass2013_13+Grass2013_14+Grass2013_15+Grass2013_16+Grass2013_17"
## [19] "Hackett2019_UK_sand_dune+Hackett2019_UK_grassland+Hackett2019_UK_heathland+Hackett2019_UK_woodland+Hackett2019_UK_salt_marsh+Hackett2019_UK_scrub"
## [20] "Neli2014"
##
## Pour la collection 5 du modèle *iid*
## [1] "olensen2002aig"
## [2] "olensen2002flo"
## [3] "vazquez2002"
## [4] "Shay2016"
## [5] "Gibson2006_GA2"
## [6] "Gibson2006_SG"
## [7] "Trojelsgaard2015_El Hierro"
## [8] "Trojelsgaard2015_Fuerteventura"
## [9] "Trojelsgaard2015_Western Sahara"
## [10] "Robinson2018"
## [11] "CordenizPicanco2018_NatFor"
## [12] "CordenizPicanco2018_SemiPast"
## [13] "CordenizPicanco2018_IntPast"
## [14] "Biella2019"
## [15] "Nel2017"
## [16] "Villalobos2019"
## [17] "LaraRomero2019_blanca+LaraRomero2019_rajada+LaraRomero2019_refugio+LaraRomero2019_torre"
## [18] "Ferrero2013"
## [19] "Sritongchuay2019_near+Sritongchuay2019_far"Et voici donc les valeurs numériques pour les \(\alpha\) (paramètres de connectivité).
Pour la collection 1 : \[\begin{bmatrix} 1 &0.83 &0.43 &0.73 &0.2 &0.5 &0.05 &0.18 \\1 &0.67 &0.36 &0.51 &0.22 &0.3 &0.05 &0.07 \\1 &0.53 &1 &0.01 &0.02 &0.89 &0 &0 \\0.97 &0.45 &0.62 &0.18 &0.47 &0.06 &0.2 &0.03 \\0.76 &0.46 &0.1 &0.27 &0.1 &0.14 &0.02 &0.03 \\0.96 &0.2 &0.37 &0.03 &0.24 &0.01 &0.09 &0.01 \\0.54 &0.28 &0.04 &0.12 &0.03 &0.05 &0.01 &0.01 \\0.69 &0.1 &0.3 &0.02 &0.06 &0.01 &0.03 &0 \\ \end{bmatrix}\] Pour la collection 2 : \[\begin{bmatrix} 0.84 &0.69 &0.13 &0.32 \\0.71 &0.49 &0.11 &0.14 \\0.54 &0.26 &0.14 &0.05 \\0.26 &0.07 &0.14 &0.01 \\ \end{bmatrix}\] Pour la collection 3 : \[\begin{bmatrix} 0.87 &0.33 \\0.11 &0.09 \\ \end{bmatrix}\] Pour la collection 4 : \[\begin{bmatrix} 0.96 &0.83 &0.96 &0.39 &0.8 &0.16 &0.66 \\0.98 &0.86 &0.83 &0.51 &0.56 &0.19 &0.09 \\0.8 &0.46 &0.74 &0.12 &0.4 &0.05 &0.13 \\0.89 &0.69 &0.44 &0.35 &0.15 &0.07 &0.01 \\0.7 &0.29 &0.35 &0.03 &0.15 &0.01 &0.03 \\0.66 &0.43 &0.1 &0.17 &0.03 &0.02 &0 \\0.32 &0.12 &0.02 &0.04 &0 &0 &0 \\ \end{bmatrix}\] Pour la collection 5 : \[\begin{bmatrix} 0.71 &0.9 &0.57 &0.83 \\0.74 &0.22 &0.7 &0.33 \\0.09 &0.44 &0.07 &0.02 \\ \end{bmatrix}\]
Répartition dans les clusters selon la taxonomie
## `summarise()` has grouped output by 'col_id', 'taxo'. You can override using
## the `.groups` argument.
## `summarise()` has grouped output by 'col_id', 'taxo'. You can override using
## the `.groups` argument.
Pollinators repartition for the iid model regarding taxonomy
## Warning: Removed 7 rows containing missing values (`geom_bar()`).
Pollinators repartition for the iid model regarding taxonomy
Plants repartition for the iid model regarding taxonomy
## Warning: Removed 63 rows containing missing values (`geom_bar()`).
Plants repartition for the iid model regarding taxonomy
Clustering avec le modèle pi
Avec le modèle pi nous obtenons les 2 collections suivantes:
| collection_id | net_id |
|---|---|
| 1 | arroyo1982_1+arroyo1982_2+arroyo3 |
| 1 | eberling1999 |
| 1 | inouye1988 |
| 1 | kato1990 |
| 1 | ramirez1992 |
| 1 | petanidou1991 |
| 1 | ramirez1989 |
| 1 | smith-ramirez2005 |
| 1 | Junker2013 |
| 1 | Kaiser_control+Kaiser_restored |
| 1 | bartomeus2008 |
| 1 | Olito-Fox2014 |
| 1 | Benadi2013_1(950m)+Benadi2013_2(1170m)+Benadi2013_6(2020m) |
| 1 | Benadi2013_3(1340m) |
| 1 | Benadi2013_4(1700m)+Benadi2013_5(1800m) |
| 1 | Kaiser-Bunbury2017_Bernica+Kaiser-Bunbury2017_Casse-dent+Kaiser-Bunbury2017_Copolia+Kaiser-Bunbury2017_La-Reserve+Kaiser-Bunbury2017_Rosebelle+Kaiser-Bunbury2017_Salazie+Kaiser-Bunbury2017_Tea-Plantation+Kaiser-Bunbury2017_Trois-Freres |
| 1 | Fang2012 |
| 1 | Shay2016 |
| 1 | Struck1994 |
| 1 | Kato2000 |
| 1 | Aizen2008_Cerro Otto_U+Aizen2008_Cerro Otto_D |
| 1 | Aizen2008_Llao-llao_U+Aizen2008_Llao-llao_D |
| 1 | Aizen2008_Puerto Blest_U+Aizen2008_Puerto Blest_D |
| 1 | Albrecht2010_49yr+Albrecht2010_63yr+Albrecht2010_84yr+Albrecht2010_109yr+Albrecht2010_130yr |
| 1 | Baldock2011_TB+Baldock2011_JN |
| 1 | Chamberlain_cr1+Chamberlain_cr2+Chamberlain_fs1+Chamberlain_fs2+Chamberlain_go1+Chamberlain_go2+Chamberlain_mm1+Chamberlain_mm2+Chamberlain_mz1+Chamberlain_mz2+Chamberlain_sm1+Chamberlain_sm2 |
| 1 | Chamberlain_HLU+Chamberlain_HLG+Chamberlain_OKU+Chamberlain_OKG+Chamberlain_WLU+Chamberlain_WLG+Chamberlain_SOU+Chamberlain_SOG |
| 1 | Chamberlain_Site1+Chamberlain_Site2+Chamberlain_Site3+Chamberlain_Site4+Chamberlain_Site5+Chamberlain_Site6 |
| 1 | Dattilo2016 |
| 1 | Devoto2005_PP+Devoto2005_AP |
| 1 | Devoto2005_VT |
| 1 | Devoto2005_LL+Devoto2005_CT |
| 1 | Dupont2009_IsenBjerg+Dupont2009_Other |
| 1 | Freitas2006 |
| 1 | Gibson2006_TA1 |
| 1 | Gibson2006_TA2 |
| 1 | Jedrzejewska2013_Ochata+Jedrzejewska2013_Kabaty |
| 1 | LaraRomero2016_pe?alara_EP+LaraRomero2016_pe?alara_PA+LaraRomero2016_nevero_EP+LaraRomero2016_nevero_PA |
| 1 | LemusJimenez2003 |
| 1 | Marrero2013 |
| 1 | MonteroCastano2017_Albufera+MonteroCastano2017_Llimpa+MonteroCastano2017_Tirant |
| 1 | Kehinde2014_Joostenberg_Conv+Kehinde2014_Joostenberg_Org+Kehinde2014_Joostenberg_Nat+Kehinde2014_Laibach_Conv+Kehinde2014_Laibach_Org+Kehinde2014_Laibach_Nat+Kehinde2014_Spier_Conv+Kehinde2014_Spier_Nat |
| 1 | Pinheiro2008 |
| 1 | Trojelsgaard2015_La Gomera |
| 1 | Trojelsgaard2015_Tenerife Teno Bajo+Trojelsgaard2015_Tenerife Fasnia |
| 1 | Vanbergen2013_balfarm+Vanbergen2013_bridgend+Vanbergen2013_dalhaikie+Vanbergen2013_netherton+Vanbergen2013_backhill+Vanbergen2013_corntulloch+Vanbergen2013_allancreich |
| 1 | Zackenberg |
| 1 | Yoshihara2008 |
| 1 | Watts2016_Chicon+Watts2016_Mantanay+Watts2016_Choquebamba+Watts2016_Huaran+Watts2016_Piscacucho+Watts2016_Poques+Watts2016_Pumamarca+Watts2016_Tiaparo+Watts2016_Yanacocha |
| 1 | Kato1993 |
| 1 | KatoMiura1996 |
| 1 | Kakutani1990 |
| 1 | Inoue1990 |
| 1 | Fragoso_RA2+Fragoso_RA3+Fragoso_RD1+Fragoso_RD3 |
| 1 | PopicThesis |
| 1 | Pfeiffer_CNE+Pfeiffer_CNM+Pfeiffer_CNT+Pfeiffer_CPB+Pfeiffer_CPM+Pfeiffer_CPR+Pfeiffer_CPS+Pfeiffer_M2+Pfeiffer_RP1+Pfeiffer_RP2+Pfeiffer_LM+Pfeiffer_LO+Pfeiffer_BD+Pfeiffer_BH+Pfeiffer_BS |
| 1 | Carstensen_Gigante+Carstensen_Paulino+Carstensen_Tinkerbell+Carstensen_Midway+Carstensen_Cedro+Carstensen_Elefante+Carstensen_Soizig |
| 1 | Orford_B1+Orford_B2+Orford_B3+Orford_B4+Orford_B5+Orford_B10 |
| 1 | Orford_B6+Orford_B7+Orford_B8+Orford_B9 |
| 1 | Blumel2016 |
| 1 | Welti_ID+Welti_K1B+Welti_K4A+Welti_4B+Welti_20B+Welti_20C+Welti_N1A+Welti_N1B+Welti_N4A+Welti_N4B+Welti_N20A+Welti_N20B |
| 1 | Souza_cerrado |
| 1 | Souza_chaco |
| 1 | Souza_pantanal |
| 1 | Souza_vereda |
| 1 | Grass2013_1+Grass2013_2+Grass2013_3+Grass2013_4+Grass2013_5+Grass2013_6+Grass2013_7+Grass2013_8+Grass2013_9+Grass2013_10+Grass2013_11+Grass2013_12+Grass2013_13+Grass2013_14+Grass2013_15+Grass2013_16+Grass2013_17 |
| 1 | Bennett2018 |
| 1 | Adedoja2018b_baseZone+Adedoja2018b_MidZone+Adedoja2018b_HighZone+Adedoja2018b_PeakZone |
| 1 | Adedoja2019 |
| 1 | CordenizPicanco2018_NatVeg |
| 1 | Benadi2018 |
| 1 | Hackett2019_NZ_salt_marsh+Hackett2019_NZ_sand_dune+Hackett2019_NZ_scrub_coprosma |
| 1 | Oleques2019 |
| 1 | Jolls2019 |
| 1 | Traveset2013_Fernandina |
| 1 | Traveset2013_Santiago |
| 1 | Traveset2013_SantaCruz |
| 1 | Traveset2013_SanCristobal |
| 1 | Simanonok2014 |
| 1 | Son2019_a1+Son2019_a2+Son2019_a3+Son2019_a4+Son2019_a5+Son2019_a6+Son2019_a7+Son2019_a8+Son2019_F1+Son2019_F2+Son2019_F3+Son2019_F4+Son2019_F5+Son2019_F6+Son2019_F7+Son2019_F8 |
| 1 | Baldock2019_Bristol |
| 1 | Baldock2019_Edinburgh |
| 1 | Baldock2019_Leeds |
| 1 | Baldock2019_Reading |
| collection_id | net_id |
|---|---|
| 2 | dupont2003 |
| 2 | herrera1988 |
| 2 | medan2002ld |
| 2 | medan2002rb |
| 2 | olensen2002aig |
| 2 | olensen2002flo |
| 2 | small1976 |
| 2 | vazquez2002 |
| 2 | Burkle2013 |
| 2 | Weiner2011 |
| 2 | Gilarranz2014_amarante+Gilarranz2014_barrosa+Gilarranz2014_cincocerros+Gilarranz2014_difuntito+Gilarranz2014_difuntos+Gilarranz2014_elmorro+Gilarranz2014_labrava+Gilarranz2014_lachata+Gilarranz2014_lapaja+Gilarranz2014_piedraalta+Gilarranz2014_vigilancia+Gilarranz2014_volcan |
| 2 | Aizen2008_Challhuaco_U+Aizen2008_Challhuaco_D |
| 2 | Devoto2005_LQ |
| 2 | Devoto2005_LT+Devoto2005_LH |
| 2 | Gibson2006_GA1 |
| 2 | Gibson2006_GA2 |
| 2 | Gibson2006_SG |
| 2 | Lundgren2005 |
| 2 | Trojelsgaard2015_El Hierro |
| 2 | Trojelsgaard2015_Gran Canaria |
| 2 | Trojelsgaard2015_Fuerteventura |
| 2 | Trojelsgaard2015_Western Sahara |
| 2 | Fragoso_RA1+Fragoso_RD2 |
| 2 | Pornon2017 |
| 2 | Kantsa2018 |
| 2 | Robinson2018 |
| 2 | CordenizPicanco2018_NatFor |
| 2 | CordenizPicanco2018_ExoFor |
| 2 | CordenizPicanco2018_SemiPast |
| 2 | CordenizPicanco2018_IntPast |
| 2 | Hackett2019_UK_sand_dune+Hackett2019_UK_grassland+Hackett2019_UK_heathland+Hackett2019_UK_woodland+Hackett2019_UK_salt_marsh+Hackett2019_UK_scrub |
| 2 | Biella2019 |
| 2 | Nel2017 |
| 2 | Villalobos2019 |
| 2 | LaraRomero2019_blanca+LaraRomero2019_rajada+LaraRomero2019_refugio+LaraRomero2019_torre |
| 2 | Traveset2013_Pinta |
| 2 | Ferrero2013 |
| 2 | Neli2014 |
| 2 | Sritongchuay2019_near+Sritongchuay2019_far |
Une fois le modèle de collection appliqué nous obtenons les structures suivantes:
##
## Pour la collection 1 du modèle *pi*## Warning in RColorBrewer::brewer.pal(n, pal): n too large, allowed maximum for palette Set2 is 8
## Returning the palette you asked for with that many colors
## [1] "arroyo1982_1+arroyo1982_2+arroyo3"
## [2] "eberling1999"
## [3] "inouye1988"
## [4] "kato1990"
## [5] "ramirez1992"
## [6] "petanidou1991"
## [7] "ramirez1989"
## [8] "smith-ramirez2005"
## [9] "Junker2013"
## [10] "Kaiser_control+Kaiser_restored"
## [11] "bartomeus2008"
## [12] "Olito-Fox2014"
## [13] "Benadi2013_1(950m)+Benadi2013_2(1170m)+Benadi2013_6(2020m)"
## [14] "Benadi2013_3(1340m)"
## [15] "Benadi2013_4(1700m)+Benadi2013_5(1800m)"
## [16] "Kaiser-Bunbury2017_Bernica+Kaiser-Bunbury2017_Casse-dent+Kaiser-Bunbury2017_Copolia+Kaiser-Bunbury2017_La-Reserve+Kaiser-Bunbury2017_Rosebelle+Kaiser-Bunbury2017_Salazie+Kaiser-Bunbury2017_Tea-Plantation+Kaiser-Bunbury2017_Trois-Freres"
## [17] "Fang2012"
## [18] "Shay2016"
## [19] "Struck1994"
## [20] "Kato2000"
## [21] "Aizen2008_Cerro Otto_U+Aizen2008_Cerro Otto_D"
## [22] "Aizen2008_Llao-llao_U+Aizen2008_Llao-llao_D"
## [23] "Aizen2008_Puerto Blest_U+Aizen2008_Puerto Blest_D"
## [24] "Albrecht2010_49yr+Albrecht2010_63yr+Albrecht2010_84yr+Albrecht2010_109yr+Albrecht2010_130yr"
## [25] "Baldock2011_TB+Baldock2011_JN"
## [26] "Chamberlain_cr1+Chamberlain_cr2+Chamberlain_fs1+Chamberlain_fs2+Chamberlain_go1+Chamberlain_go2+Chamberlain_mm1+Chamberlain_mm2+Chamberlain_mz1+Chamberlain_mz2+Chamberlain_sm1+Chamberlain_sm2"
## [27] "Chamberlain_HLU+Chamberlain_HLG+Chamberlain_OKU+Chamberlain_OKG+Chamberlain_WLU+Chamberlain_WLG+Chamberlain_SOU+Chamberlain_SOG"
## [28] "Chamberlain_Site1+Chamberlain_Site2+Chamberlain_Site3+Chamberlain_Site4+Chamberlain_Site5+Chamberlain_Site6"
## [29] "Dattilo2016"
## [30] "Devoto2005_PP+Devoto2005_AP"
## [31] "Devoto2005_VT"
## [32] "Devoto2005_LL+Devoto2005_CT"
## [33] "Dupont2009_IsenBjerg+Dupont2009_Other"
## [34] "Freitas2006"
## [35] "Gibson2006_TA1"
## [36] "Gibson2006_TA2"
## [37] "Jedrzejewska2013_Ochata+Jedrzejewska2013_Kabaty"
## [38] "LaraRomero2016_pe?alara_EP+LaraRomero2016_pe?alara_PA+LaraRomero2016_nevero_EP+LaraRomero2016_nevero_PA"
## [39] "LemusJimenez2003"
## [40] "Marrero2013"
## [41] "MonteroCastano2017_Albufera+MonteroCastano2017_Llimpa+MonteroCastano2017_Tirant"
## [42] "Kehinde2014_Joostenberg_Conv+Kehinde2014_Joostenberg_Org+Kehinde2014_Joostenberg_Nat+Kehinde2014_Laibach_Conv+Kehinde2014_Laibach_Org+Kehinde2014_Laibach_Nat+Kehinde2014_Spier_Conv+Kehinde2014_Spier_Nat"
## [43] "Pinheiro2008"
## [44] "Trojelsgaard2015_La Gomera"
## [45] "Trojelsgaard2015_Tenerife Teno Bajo+Trojelsgaard2015_Tenerife Fasnia"
## [46] "Vanbergen2013_balfarm+Vanbergen2013_bridgend+Vanbergen2013_dalhaikie+Vanbergen2013_netherton+Vanbergen2013_backhill+Vanbergen2013_corntulloch+Vanbergen2013_allancreich"
## [47] "Zackenberg"
## [48] "Yoshihara2008"
## [49] "Watts2016_Chicon+Watts2016_Mantanay+Watts2016_Choquebamba+Watts2016_Huaran+Watts2016_Piscacucho+Watts2016_Poques+Watts2016_Pumamarca+Watts2016_Tiaparo+Watts2016_Yanacocha"
## [50] "Kato1993"
## [51] "KatoMiura1996"
## [52] "Kakutani1990"
## [53] "Inoue1990"
## [54] "Fragoso_RA2+Fragoso_RA3+Fragoso_RD1+Fragoso_RD3"
## [55] "PopicThesis"
## [56] "Pfeiffer_CNE+Pfeiffer_CNM+Pfeiffer_CNT+Pfeiffer_CPB+Pfeiffer_CPM+Pfeiffer_CPR+Pfeiffer_CPS+Pfeiffer_M2+Pfeiffer_RP1+Pfeiffer_RP2+Pfeiffer_LM+Pfeiffer_LO+Pfeiffer_BD+Pfeiffer_BH+Pfeiffer_BS"
## [57] "Carstensen_Gigante+Carstensen_Paulino+Carstensen_Tinkerbell+Carstensen_Midway+Carstensen_Cedro+Carstensen_Elefante+Carstensen_Soizig"
## [58] "Orford_B1+Orford_B2+Orford_B3+Orford_B4+Orford_B5+Orford_B10"
## [59] "Orford_B6+Orford_B7+Orford_B8+Orford_B9"
## [60] "Blumel2016"
## [61] "Welti_ID+Welti_K1B+Welti_K4A+Welti_4B+Welti_20B+Welti_20C+Welti_N1A+Welti_N1B+Welti_N4A+Welti_N4B+Welti_N20A+Welti_N20B"
## [62] "Souza_cerrado"
## [63] "Souza_chaco"
## [64] "Souza_pantanal"
## [65] "Souza_vereda"
## [66] "Grass2013_1+Grass2013_2+Grass2013_3+Grass2013_4+Grass2013_5+Grass2013_6+Grass2013_7+Grass2013_8+Grass2013_9+Grass2013_10+Grass2013_11+Grass2013_12+Grass2013_13+Grass2013_14+Grass2013_15+Grass2013_16+Grass2013_17"
## [67] "Bennett2018"
## [68] "Adedoja2018b_baseZone+Adedoja2018b_MidZone+Adedoja2018b_HighZone+Adedoja2018b_PeakZone"
## [69] "Adedoja2019"
## [70] "CordenizPicanco2018_NatVeg"
## [71] "Benadi2018"
## [72] "Hackett2019_NZ_salt_marsh+Hackett2019_NZ_sand_dune+Hackett2019_NZ_scrub_coprosma"
## [73] "Oleques2019"
## [74] "Jolls2019"
## [75] "Traveset2013_Fernandina"
## [76] "Traveset2013_Santiago"
## [77] "Traveset2013_SantaCruz"
## [78] "Traveset2013_SanCristobal"
## [79] "Simanonok2014"
## [80] "Son2019_a1+Son2019_a2+Son2019_a3+Son2019_a4+Son2019_a5+Son2019_a6+Son2019_a7+Son2019_a8+Son2019_F1+Son2019_F2+Son2019_F3+Son2019_F4+Son2019_F5+Son2019_F6+Son2019_F7+Son2019_F8"
## [81] "Baldock2019_Bristol"
## [82] "Baldock2019_Edinburgh"
## [83] "Baldock2019_Leeds"
## [84] "Baldock2019_Reading"
##
## Pour la collection 2 du modèle *pi*
## [1] "dupont2003"
## [2] "herrera1988"
## [3] "medan2002ld"
## [4] "medan2002rb"
## [5] "olensen2002aig"
## [6] "olensen2002flo"
## [7] "small1976"
## [8] "vazquez2002"
## [9] "Burkle2013"
## [10] "Weiner2011"
## [11] "Gilarranz2014_amarante+Gilarranz2014_barrosa+Gilarranz2014_cincocerros+Gilarranz2014_difuntito+Gilarranz2014_difuntos+Gilarranz2014_elmorro+Gilarranz2014_labrava+Gilarranz2014_lachata+Gilarranz2014_lapaja+Gilarranz2014_piedraalta+Gilarranz2014_vigilancia+Gilarranz2014_volcan"
## [12] "Aizen2008_Challhuaco_U+Aizen2008_Challhuaco_D"
## [13] "Devoto2005_LQ"
## [14] "Devoto2005_LT+Devoto2005_LH"
## [15] "Gibson2006_GA1"
## [16] "Gibson2006_GA2"
## [17] "Gibson2006_SG"
## [18] "Lundgren2005"
## [19] "Trojelsgaard2015_El Hierro"
## [20] "Trojelsgaard2015_Gran Canaria"
## [21] "Trojelsgaard2015_Fuerteventura"
## [22] "Trojelsgaard2015_Western Sahara"
## [23] "Fragoso_RA1+Fragoso_RD2"
## [24] "Pornon2017"
## [25] "Kantsa2018"
## [26] "Robinson2018"
## [27] "CordenizPicanco2018_NatFor"
## [28] "CordenizPicanco2018_ExoFor"
## [29] "CordenizPicanco2018_SemiPast"
## [30] "CordenizPicanco2018_IntPast"
## [31] "Hackett2019_UK_sand_dune+Hackett2019_UK_grassland+Hackett2019_UK_heathland+Hackett2019_UK_woodland+Hackett2019_UK_salt_marsh+Hackett2019_UK_scrub"
## [32] "Biella2019"
## [33] "Nel2017"
## [34] "Villalobos2019"
## [35] "LaraRomero2019_blanca+LaraRomero2019_rajada+LaraRomero2019_refugio+LaraRomero2019_torre"
## [36] "Traveset2013_Pinta"
## [37] "Ferrero2013"
## [38] "Neli2014"
## [39] "Sritongchuay2019_near+Sritongchuay2019_far"Et voici donc les valeurs numériques pour les \(\alpha\) (paramètres de connectivité).
Pour la collection 1 : \[\begin{bmatrix} 1 &0.9 &0.92 &0.55 &0.75 &0.57 &0.17 \\0.1 &0.21 &0.81 &0.86 &0.7 &0.4 &0.54 \\0.38 &0.12 &0.03 &0.09 &0.92 &0.65 &0.17 \\0.76 &0.5 &0.1 &0.33 &0.17 &0.04 &0.65 \\0.71 &0.5 &0.18 &0.28 &0.19 &0.04 &0.01 \\0.03 &0.89 &0.4 &0.05 &0.53 &0.2 &0.03 \\0.22 &0.07 &0.01 &0.22 &0.35 &0.21 &0.06 \\0.11 &0.07 &0.01 &0.01 &0.01 &0.6 &0.15 \\0.02 &0.21 &0.06 &0.01 &0.06 &0.01 &0 \\ \end{bmatrix}\] Pour la collection 2 : \[\begin{bmatrix} 0.84 &0.99 &0.66 &0.99 &0.38 &0.79 \\0.79 &0.5 &0.01 &0.19 &0.46 &0.51 \\0.15 &0.02 &0.08 &0.83 &0.22 &0.44 \\0 &0.05 &0.49 &0.07 &0.15 &0 \\0.01 &0.16 &0 &0.04 &0 &0 \\ \end{bmatrix}\]
Répartition dans les clusters selon la taxonomie
## `summarise()` has grouped output by 'col_id', 'taxo'. You can override using
## the `.groups` argument.
## `summarise()` has grouped output by 'col_id', 'taxo'. You can override using
## the `.groups` argument.
Pollinators repartition for the pi model regarding taxonomy
Pollinators repartition for the pi model regarding taxonomy
Plants repartition for the pi model regarding taxonomy
## Warning: Removed 45 rows containing missing values (`geom_bar()`).
Plants repartition for the pi model regarding taxonomy
Clustering avec le modèle rho
Avec le modèle rho nous obtenons les 83 collections suivantes:
| x |
|---|
| arroyo1982_1+arroyo1982_2+arroyo3 |
| dupont2003 |
| eberling1999 |
| herrera1988 |
| inouye1988 |
| kato1990 |
| medan2002ld |
| medan2002rb |
| olensen2002aig |
| olensen2002flo |
| ramirez1992 |
| small1976 |
| vazquez2002 |
| petanidou1991 |
| ramirez1989 |
| smith-ramirez2005 |
| Burkle2013 |
| Junker2013 |
| Weiner2011 |
| Kaiser_control+Kaiser_restored |
| bartomeus2008 |
| Olito-Fox2014 |
| Gilarranz2014_amarante+Gilarranz2014_barrosa+Gilarranz2014_cincocerros+Gilarranz2014_difuntito+Gilarranz2014_difuntos+Gilarranz2014_elmorro+Gilarranz2014_labrava+Gilarranz2014_lachata+Gilarranz2014_lapaja+Gilarranz2014_piedraalta+Gilarranz2014_vigilancia+Gilarranz2014_volcan |
| Benadi2013_1(950m)+Benadi2013_2(1170m)+Benadi2013_6(2020m) |
| Benadi2013_3(1340m) |
| Benadi2013_4(1700m)+Benadi2013_5(1800m) |
| Kaiser-Bunbury2017_Bernica+Kaiser-Bunbury2017_Casse-dent+Kaiser-Bunbury2017_Copolia+Kaiser-Bunbury2017_La-Reserve+Kaiser-Bunbury2017_Rosebelle+Kaiser-Bunbury2017_Salazie+Kaiser-Bunbury2017_Tea-Plantation+Kaiser-Bunbury2017_Trois-Freres |
| Fang2012 |
| Shay2016 |
| Struck1994 |
| Kato2000 |
| Aizen2008_Challhuaco_U+Aizen2008_Challhuaco_D |
| Aizen2008_Cerro Otto_U+Aizen2008_Cerro Otto_D |
| Aizen2008_Llao-llao_U+Aizen2008_Llao-llao_D |
| Aizen2008_Puerto Blest_U+Aizen2008_Puerto Blest_D |
| Albrecht2010_49yr+Albrecht2010_63yr+Albrecht2010_84yr+Albrecht2010_109yr+Albrecht2010_130yr |
| Baldock2011_TB+Baldock2011_JN |
| Chamberlain_cr1+Chamberlain_cr2+Chamberlain_fs1+Chamberlain_fs2+Chamberlain_go1+Chamberlain_go2+Chamberlain_mm1+Chamberlain_mm2+Chamberlain_mz1+Chamberlain_mz2+Chamberlain_sm1+Chamberlain_sm2 |
| Chamberlain_HLU+Chamberlain_HLG+Chamberlain_OKU+Chamberlain_OKG+Chamberlain_WLU+Chamberlain_WLG+Chamberlain_SOU+Chamberlain_SOG |
| Chamberlain_Site1+Chamberlain_Site2+Chamberlain_Site3+Chamberlain_Site4+Chamberlain_Site5+Chamberlain_Site6 |
| Dattilo2016 |
| Devoto2005_LQ |
| Devoto2005_PP+Devoto2005_AP |
| Devoto2005_LT+Devoto2005_LH |
| Devoto2005_VT |
| Devoto2005_LL+Devoto2005_CT |
| Dupont2009_IsenBjerg+Dupont2009_Other |
| Freitas2006 |
| Gibson2006_GA1 |
| Gibson2006_GA2 |
| Gibson2006_SG |
| Gibson2006_TA1 |
| Gibson2006_TA2 |
| Jedrzejewska2013_Ochata+Jedrzejewska2013_Kabaty |
| LaraRomero2016_pe?alara_EP+LaraRomero2016_pe?alara_PA+LaraRomero2016_nevero_EP+LaraRomero2016_nevero_PA |
| LemusJimenez2003 |
| Lundgren2005 |
| Marrero2013 |
| MonteroCastano2017_Albufera+MonteroCastano2017_Llimpa+MonteroCastano2017_Tirant |
| Kehinde2014_Joostenberg_Conv+Kehinde2014_Joostenberg_Org+Kehinde2014_Joostenberg_Nat+Kehinde2014_Laibach_Conv+Kehinde2014_Laibach_Org+Kehinde2014_Laibach_Nat+Kehinde2014_Spier_Conv+Kehinde2014_Spier_Nat |
| Pinheiro2008 |
| Trojelsgaard2015_El Hierro |
| Trojelsgaard2015_La Gomera |
| Trojelsgaard2015_Gran Canaria |
| Trojelsgaard2015_Fuerteventura |
| Trojelsgaard2015_Tenerife Teno Bajo+Trojelsgaard2015_Tenerife Fasnia |
| Trojelsgaard2015_Western Sahara |
| Vanbergen2013_balfarm+Vanbergen2013_bridgend+Vanbergen2013_dalhaikie+Vanbergen2013_netherton+Vanbergen2013_backhill+Vanbergen2013_corntulloch+Vanbergen2013_allancreich |
| Zackenberg |
| Yoshihara2008 |
| Watts2016_Chicon+Watts2016_Mantanay+Watts2016_Choquebamba+Watts2016_Huaran+Watts2016_Piscacucho+Watts2016_Poques+Watts2016_Pumamarca+Watts2016_Tiaparo+Watts2016_Yanacocha |
| Kato1993 |
| KatoMiura1996 |
| Kakutani1990 |
| Inoue1990 |
| Fragoso_RA1+Fragoso_RD2 |
| Fragoso_RA2+Fragoso_RA3+Fragoso_RD1+Fragoso_RD3 |
| PopicThesis |
| Pfeiffer_CNE+Pfeiffer_CNM+Pfeiffer_CNT+Pfeiffer_CPB+Pfeiffer_CPM+Pfeiffer_CPR+Pfeiffer_CPS+Pfeiffer_M2+Pfeiffer_RP1+Pfeiffer_RP2+Pfeiffer_LM+Pfeiffer_LO+Pfeiffer_BD+Pfeiffer_BH+Pfeiffer_BS |
| Carstensen_Gigante+Carstensen_Paulino+Carstensen_Tinkerbell+Carstensen_Midway+Carstensen_Cedro+Carstensen_Elefante+Carstensen_Soizig |
| Pornon2017 |
| Orford_B1+Orford_B2+Orford_B3+Orford_B4+Orford_B5+Orford_B10 |
| Orford_B6+Orford_B7+Orford_B8+Orford_B9 |
| Blumel2016 |
| Welti_ID+Welti_K1B+Welti_K4A+Welti_4B+Welti_20B+Welti_20C+Welti_N1A+Welti_N1B+Welti_N4A+Welti_N4B+Welti_N20A+Welti_N20B |
| Kantsa2018 |
| Souza_cerrado |
| Souza_chaco |
| Souza_pantanal |
| Souza_vereda |
| Grass2013_1+Grass2013_2+Grass2013_3+Grass2013_4+Grass2013_5+Grass2013_6+Grass2013_7+Grass2013_8+Grass2013_9+Grass2013_10+Grass2013_11+Grass2013_12+Grass2013_13+Grass2013_14+Grass2013_15+Grass2013_16+Grass2013_17 |
| Robinson2018 |
| Bennett2018 |
| Adedoja2018b_baseZone+Adedoja2018b_MidZone+Adedoja2018b_HighZone+Adedoja2018b_PeakZone |
| Adedoja2019 |
| CordenizPicanco2018_NatFor |
| CordenizPicanco2018_NatVeg |
| CordenizPicanco2018_ExoFor |
| CordenizPicanco2018_SemiPast |
| CordenizPicanco2018_IntPast |
| Benadi2018 |
| Hackett2019_NZ_salt_marsh+Hackett2019_NZ_sand_dune+Hackett2019_NZ_scrub_coprosma |
| Hackett2019_UK_sand_dune+Hackett2019_UK_grassland+Hackett2019_UK_heathland+Hackett2019_UK_woodland+Hackett2019_UK_salt_marsh+Hackett2019_UK_scrub |
| Oleques2019 |
| Biella2019 |
| Jolls2019 |
| Nel2017 |
| Villalobos2019 |
| LaraRomero2019_blanca+LaraRomero2019_rajada+LaraRomero2019_refugio+LaraRomero2019_torre |
| Traveset2013_Fernandina |
| Traveset2013_Pinta |
| Traveset2013_Santiago |
| Traveset2013_SantaCruz |
| Traveset2013_SanCristobal |
| Ferrero2013 |
| Simanonok2014 |
| Son2019_a1+Son2019_a2+Son2019_a3+Son2019_a4+Son2019_a5+Son2019_a6+Son2019_a7+Son2019_a8+Son2019_F1+Son2019_F2+Son2019_F3+Son2019_F4+Son2019_F5+Son2019_F6+Son2019_F7+Son2019_F8 |
| Neli2014 |
| Sritongchuay2019_near+Sritongchuay2019_far |
| Baldock2019_Bristol |
| Baldock2019_Edinburgh |
| Baldock2019_Leeds |
| Baldock2019_Reading |
Une fois le modèle de collection appliqué nous obtenons les structures suivantes:
##
## Pour la collection 1 du modèle *rho*
## [1] "arroyo1982_1+arroyo1982_2+arroyo3"
## [2] "dupont2003"
## [3] "eberling1999"
## [4] "herrera1988"
## [5] "inouye1988"
## [6] "kato1990"
## [7] "medan2002ld"
## [8] "medan2002rb"
## [9] "olensen2002aig"
## [10] "olensen2002flo"
## [11] "ramirez1992"
## [12] "small1976"
## [13] "vazquez2002"
## [14] "petanidou1991"
## [15] "ramirez1989"
## [16] "smith-ramirez2005"
## [17] "Burkle2013"
## [18] "Junker2013"
## [19] "Weiner2011"
## [20] "Kaiser_control+Kaiser_restored"
## [21] "bartomeus2008"
## [22] "Olito-Fox2014"
## [23] "Gilarranz2014_amarante+Gilarranz2014_barrosa+Gilarranz2014_cincocerros+Gilarranz2014_difuntito+Gilarranz2014_difuntos+Gilarranz2014_elmorro+Gilarranz2014_labrava+Gilarranz2014_lachata+Gilarranz2014_lapaja+Gilarranz2014_piedraalta+Gilarranz2014_vigilancia+Gilarranz2014_volcan"
## [24] "Benadi2013_1(950m)+Benadi2013_2(1170m)+Benadi2013_6(2020m)"
## [25] "Benadi2013_3(1340m)"
## [26] "Benadi2013_4(1700m)+Benadi2013_5(1800m)"
## [27] "Kaiser-Bunbury2017_Bernica+Kaiser-Bunbury2017_Casse-dent+Kaiser-Bunbury2017_Copolia+Kaiser-Bunbury2017_La-Reserve+Kaiser-Bunbury2017_Rosebelle+Kaiser-Bunbury2017_Salazie+Kaiser-Bunbury2017_Tea-Plantation+Kaiser-Bunbury2017_Trois-Freres"
## [28] "Fang2012"
## [29] "Shay2016"
## [30] "Struck1994"
## [31] "Kato2000"
## [32] "Aizen2008_Challhuaco_U+Aizen2008_Challhuaco_D"
## [33] "Aizen2008_Cerro Otto_U+Aizen2008_Cerro Otto_D"
## [34] "Aizen2008_Llao-llao_U+Aizen2008_Llao-llao_D"
## [35] "Aizen2008_Puerto Blest_U+Aizen2008_Puerto Blest_D"
## [36] "Albrecht2010_49yr+Albrecht2010_63yr+Albrecht2010_84yr+Albrecht2010_109yr+Albrecht2010_130yr"
## [37] "Baldock2011_TB+Baldock2011_JN"
## [38] "Chamberlain_cr1+Chamberlain_cr2+Chamberlain_fs1+Chamberlain_fs2+Chamberlain_go1+Chamberlain_go2+Chamberlain_mm1+Chamberlain_mm2+Chamberlain_mz1+Chamberlain_mz2+Chamberlain_sm1+Chamberlain_sm2"
## [39] "Chamberlain_HLU+Chamberlain_HLG+Chamberlain_OKU+Chamberlain_OKG+Chamberlain_WLU+Chamberlain_WLG+Chamberlain_SOU+Chamberlain_SOG"
## [40] "Chamberlain_Site1+Chamberlain_Site2+Chamberlain_Site3+Chamberlain_Site4+Chamberlain_Site5+Chamberlain_Site6"
## [41] "Dattilo2016"
## [42] "Devoto2005_LQ"
## [43] "Devoto2005_PP+Devoto2005_AP"
## [44] "Devoto2005_LT+Devoto2005_LH"
## [45] "Devoto2005_VT"
## [46] "Devoto2005_LL+Devoto2005_CT"
## [47] "Dupont2009_IsenBjerg+Dupont2009_Other"
## [48] "Freitas2006"
## [49] "Gibson2006_GA1"
## [50] "Gibson2006_GA2"
## [51] "Gibson2006_SG"
## [52] "Gibson2006_TA1"
## [53] "Gibson2006_TA2"
## [54] "Jedrzejewska2013_Ochata+Jedrzejewska2013_Kabaty"
## [55] "LaraRomero2016_pe?alara_EP+LaraRomero2016_pe?alara_PA+LaraRomero2016_nevero_EP+LaraRomero2016_nevero_PA"
## [56] "LemusJimenez2003"
## [57] "Lundgren2005"
## [58] "Marrero2013"
## [59] "MonteroCastano2017_Albufera+MonteroCastano2017_Llimpa+MonteroCastano2017_Tirant"
## [60] "Kehinde2014_Joostenberg_Conv+Kehinde2014_Joostenberg_Org+Kehinde2014_Joostenberg_Nat+Kehinde2014_Laibach_Conv+Kehinde2014_Laibach_Org+Kehinde2014_Laibach_Nat+Kehinde2014_Spier_Conv+Kehinde2014_Spier_Nat"
## [61] "Pinheiro2008"
## [62] "Trojelsgaard2015_El Hierro"
## [63] "Trojelsgaard2015_La Gomera"
## [64] "Trojelsgaard2015_Gran Canaria"
## [65] "Trojelsgaard2015_Fuerteventura"
## [66] "Trojelsgaard2015_Tenerife Teno Bajo+Trojelsgaard2015_Tenerife Fasnia"
## [67] "Trojelsgaard2015_Western Sahara"
## [68] "Vanbergen2013_balfarm+Vanbergen2013_bridgend+Vanbergen2013_dalhaikie+Vanbergen2013_netherton+Vanbergen2013_backhill+Vanbergen2013_corntulloch+Vanbergen2013_allancreich"
## [69] "Zackenberg"
## [70] "Yoshihara2008"
## [71] "Watts2016_Chicon+Watts2016_Mantanay+Watts2016_Choquebamba+Watts2016_Huaran+Watts2016_Piscacucho+Watts2016_Poques+Watts2016_Pumamarca+Watts2016_Tiaparo+Watts2016_Yanacocha"
## [72] "Kato1993"
## [73] "KatoMiura1996"
## [74] "Kakutani1990"
## [75] "Inoue1990"
## [76] "Fragoso_RA1+Fragoso_RD2"
## [77] "Fragoso_RA2+Fragoso_RA3+Fragoso_RD1+Fragoso_RD3"
## [78] "PopicThesis"
## [79] "Pfeiffer_CNE+Pfeiffer_CNM+Pfeiffer_CNT+Pfeiffer_CPB+Pfeiffer_CPM+Pfeiffer_CPR+Pfeiffer_CPS+Pfeiffer_M2+Pfeiffer_RP1+Pfeiffer_RP2+Pfeiffer_LM+Pfeiffer_LO+Pfeiffer_BD+Pfeiffer_BH+Pfeiffer_BS"
## [80] "Carstensen_Gigante+Carstensen_Paulino+Carstensen_Tinkerbell+Carstensen_Midway+Carstensen_Cedro+Carstensen_Elefante+Carstensen_Soizig"
## [81] "Pornon2017"
## [82] "Orford_B1+Orford_B2+Orford_B3+Orford_B4+Orford_B5+Orford_B10"
## [83] "Orford_B6+Orford_B7+Orford_B8+Orford_B9"
## [84] "Blumel2016"
## [85] "Welti_ID+Welti_K1B+Welti_K4A+Welti_4B+Welti_20B+Welti_20C+Welti_N1A+Welti_N1B+Welti_N4A+Welti_N4B+Welti_N20A+Welti_N20B"
## [86] "Kantsa2018"
## [87] "Souza_cerrado"
## [88] "Souza_chaco"
## [89] "Souza_pantanal"
## [90] "Souza_vereda"
## [91] "Grass2013_1+Grass2013_2+Grass2013_3+Grass2013_4+Grass2013_5+Grass2013_6+Grass2013_7+Grass2013_8+Grass2013_9+Grass2013_10+Grass2013_11+Grass2013_12+Grass2013_13+Grass2013_14+Grass2013_15+Grass2013_16+Grass2013_17"
## [92] "Robinson2018"
## [93] "Bennett2018"
## [94] "Adedoja2018b_baseZone+Adedoja2018b_MidZone+Adedoja2018b_HighZone+Adedoja2018b_PeakZone"
## [95] "Adedoja2019"
## [96] "CordenizPicanco2018_NatFor"
## [97] "CordenizPicanco2018_NatVeg"
## [98] "CordenizPicanco2018_ExoFor"
## [99] "CordenizPicanco2018_SemiPast"
## [100] "CordenizPicanco2018_IntPast"
## [101] "Benadi2018"
## [102] "Hackett2019_NZ_salt_marsh+Hackett2019_NZ_sand_dune+Hackett2019_NZ_scrub_coprosma"
## [103] "Hackett2019_UK_sand_dune+Hackett2019_UK_grassland+Hackett2019_UK_heathland+Hackett2019_UK_woodland+Hackett2019_UK_salt_marsh+Hackett2019_UK_scrub"
## [104] "Oleques2019"
## [105] "Biella2019"
## [106] "Jolls2019"
## [107] "Nel2017"
## [108] "Villalobos2019"
## [109] "LaraRomero2019_blanca+LaraRomero2019_rajada+LaraRomero2019_refugio+LaraRomero2019_torre"
## [110] "Traveset2013_Fernandina"
## [111] "Traveset2013_Pinta"
## [112] "Traveset2013_Santiago"
## [113] "Traveset2013_SantaCruz"
## [114] "Traveset2013_SanCristobal"
## [115] "Ferrero2013"
## [116] "Simanonok2014"
## [117] "Son2019_a1+Son2019_a2+Son2019_a3+Son2019_a4+Son2019_a5+Son2019_a6+Son2019_a7+Son2019_a8+Son2019_F1+Son2019_F2+Son2019_F3+Son2019_F4+Son2019_F5+Son2019_F6+Son2019_F7+Son2019_F8"
## [118] "Neli2014"
## [119] "Sritongchuay2019_near+Sritongchuay2019_far"
## [120] "Baldock2019_Bristol"
## [121] "Baldock2019_Edinburgh"
## [122] "Baldock2019_Leeds"
## [123] "Baldock2019_Reading"Et voici donc les valeurs numériques pour les \(\alpha\) (paramètres de connectivité).
Pour la collection 1: \[\begin{bmatrix} 0.77 &0.91 &0.64 &0.73 &0.09 &0.34 &0.98 &0.9 &0.41 \\0.63 &0.09 &0.15 &0.94 &0.56 &0.6 &0.25 &0.24 &0.05 \\0.59 &0.73 &0.19 &0.38 &0.04 &0.09 &0.51 &0.22 &0.46 \\0.07 &0.19 &0.02 &0.73 &0.58 &0.2 &0.22 &0.04 &0.03 \\0.69 &0.13 &0.34 &0.03 &0.1 &0.01 &0.53 &0.33 &0.08 \\0.09 &0.02 &0.01 &0.27 &0.06 &0.12 &0.01 &0.04 &0 \\ \end{bmatrix}\]
Répartition dans les clusters selon la taxonomie
## `summarise()` has grouped output by 'col_id', 'taxo'. You can override using
## the `.groups` argument.
## `summarise()` has grouped output by 'col_id', 'taxo'. You can override using
## the `.groups` argument.
Pollinators repartition for the rho model regarding taxonomy
Pollinators repartition for the rho model regarding taxonomy
Plants repartition for the rho model regarding taxonomy
## Warning: Removed 9 rows containing missing values (`geom_bar()`).
Plants repartition for the rho model regarding taxonomy
Clustering avec le modèle pirho
Avec le modèle pirho nous obtenons les 15 collections suivantes:
| collection_id | net_id |
|---|---|
| 1 | arroyo1982_1+arroyo1982_2+arroyo3 |
| 1 | dupont2003 |
| 1 | petanidou1991 |
| 1 | Aizen2008_Challhuaco_U+Aizen2008_Challhuaco_D |
| 1 | Aizen2008_Llao-llao_U+Aizen2008_Llao-llao_D |
| 1 | Jedrzejewska2013_Ochata+Jedrzejewska2013_Kabaty |
| 1 | Pinheiro2008 |
| 1 | Souza_pantanal |
| 1 | Robinson2018 |
| 1 | Jolls2019 |
| 1 | Traveset2013_Fernandina |
| 1 | Baldock2019_Leeds |
| 1 | Baldock2019_Reading |
| collection_id | net_id |
|---|---|
| 2 | Benadi2013_3(1340m) |
| 2 | Trojelsgaard2015_La Gomera |
| 2 | CordenizPicanco2018_SemiPast |
| collection_id | net_id |
|---|---|
| 3 | Kato2000 |
| 3 | Freitas2006 |
| 3 | Inoue1990 |
| 3 | Souza_cerrado |
| 3 | Adedoja2019 |
| 3 | Baldock2019_Bristol |
| collection_id | net_id |
|---|---|
| 4 | Aizen2008_Puerto Blest_U+Aizen2008_Puerto Blest_D |
| 4 | LemusJimenez2003 |
| collection_id | net_id |
|---|---|
| 5 | inouye1988 |
| 5 | Junker2013 |
| 5 | Kehinde2014_Joostenberg_Conv+Kehinde2014_Joostenberg_Org+Kehinde2014_Joostenberg_Nat+Kehinde2014_Laibach_Conv+Kehinde2014_Laibach_Org+Kehinde2014_Laibach_Nat+Kehinde2014_Spier_Conv+Kehinde2014_Spier_Nat |
| 5 | Watts2016_Chicon+Watts2016_Mantanay+Watts2016_Choquebamba+Watts2016_Huaran+Watts2016_Piscacucho+Watts2016_Poques+Watts2016_Pumamarca+Watts2016_Tiaparo+Watts2016_Yanacocha |
| 5 | Kakutani1990 |
| 5 | Fragoso_RA1+Fragoso_RD2 |
| 5 | Souza_chaco |
| 5 | Oleques2019 |
| collection_id | net_id |
|---|---|
| 6 | medan2002ld |
| 6 | small1976 |
| 6 | smith-ramirez2005 |
| 6 | Benadi2013_1(950m)+Benadi2013_2(1170m)+Benadi2013_6(2020m) |
| 6 | Shay2016 |
| 6 | Aizen2008_Cerro Otto_U+Aizen2008_Cerro Otto_D |
| 6 | Lundgren2005 |
| 6 | Zackenberg |
| 6 | Carstensen_Gigante+Carstensen_Paulino+Carstensen_Tinkerbell+Carstensen_Midway+Carstensen_Cedro+Carstensen_Elefante+Carstensen_Soizig |
| 6 | Welti_ID+Welti_K1B+Welti_K4A+Welti_4B+Welti_20B+Welti_20C+Welti_N1A+Welti_N1B+Welti_N4A+Welti_N4B+Welti_N20A+Welti_N20B |
| 6 | Bennett2018 |
| 6 | CordenizPicanco2018_NatFor |
| 6 | CordenizPicanco2018_ExoFor |
| 6 | CordenizPicanco2018_IntPast |
| 6 | Benadi2018 |
| 6 | Villalobos2019 |
| 6 | Traveset2013_Santiago |
| 6 | Traveset2013_SantaCruz |
| 6 | Son2019_a1+Son2019_a2+Son2019_a3+Son2019_a4+Son2019_a5+Son2019_a6+Son2019_a7+Son2019_a8+Son2019_F1+Son2019_F2+Son2019_F3+Son2019_F4+Son2019_F5+Son2019_F6+Son2019_F7+Son2019_F8 |
| 6 | Sritongchuay2019_near+Sritongchuay2019_far |
| collection_id | net_id |
|---|---|
| 7 | medan2002rb |
| 7 | olensen2002flo |
| 7 | vazquez2002 |
| 7 | Trojelsgaard2015_Gran Canaria |
| 7 | Trojelsgaard2015_Western Sahara |
| 7 | LaraRomero2019_blanca+LaraRomero2019_rajada+LaraRomero2019_refugio+LaraRomero2019_torre |
| collection_id | net_id |
|---|---|
| 8 | Weiner2011 |
| 8 | Kaiser_control+Kaiser_restored |
| 8 | Gilarranz2014_amarante+Gilarranz2014_barrosa+Gilarranz2014_cincocerros+Gilarranz2014_difuntito+Gilarranz2014_difuntos+Gilarranz2014_elmorro+Gilarranz2014_labrava+Gilarranz2014_lachata+Gilarranz2014_lapaja+Gilarranz2014_piedraalta+Gilarranz2014_vigilancia+Gilarranz2014_volcan |
| 8 | Kaiser-Bunbury2017_Bernica+Kaiser-Bunbury2017_Casse-dent+Kaiser-Bunbury2017_Copolia+Kaiser-Bunbury2017_La-Reserve+Kaiser-Bunbury2017_Rosebelle+Kaiser-Bunbury2017_Salazie+Kaiser-Bunbury2017_Tea-Plantation+Kaiser-Bunbury2017_Trois-Freres |
| 8 | Fang2012 |
| 8 | Gibson2006_SG |
| 8 | Gibson2006_TA1 |
| 8 | Trojelsgaard2015_Fuerteventura |
| 8 | Pfeiffer_CNE+Pfeiffer_CNM+Pfeiffer_CNT+Pfeiffer_CPB+Pfeiffer_CPM+Pfeiffer_CPR+Pfeiffer_CPS+Pfeiffer_M2+Pfeiffer_RP1+Pfeiffer_RP2+Pfeiffer_LM+Pfeiffer_LO+Pfeiffer_BD+Pfeiffer_BH+Pfeiffer_BS |
| 8 | Biella2019 |
| 8 | Nel2017 |
| 8 | Ferrero2013 |
| 8 | Neli2014 |
| collection_id | net_id |
|---|---|
| 9 | eberling1999 |
| 9 | ramirez1992 |
| 9 | Struck1994 |
| 9 | Albrecht2010_49yr+Albrecht2010_63yr+Albrecht2010_84yr+Albrecht2010_109yr+Albrecht2010_130yr |
| 9 | Devoto2005_PP+Devoto2005_AP |
| 9 | Devoto2005_VT |
| 9 | Gibson2006_TA2 |
| 9 | MonteroCastano2017_Albufera+MonteroCastano2017_Llimpa+MonteroCastano2017_Tirant |
| 9 | Yoshihara2008 |
| 9 | PopicThesis |
| 9 | Orford_B1+Orford_B2+Orford_B3+Orford_B4+Orford_B5+Orford_B10 |
| 9 | Souza_vereda |
| 9 | Adedoja2018b_baseZone+Adedoja2018b_MidZone+Adedoja2018b_HighZone+Adedoja2018b_PeakZone |
| 9 | Hackett2019_NZ_salt_marsh+Hackett2019_NZ_sand_dune+Hackett2019_NZ_scrub_coprosma |
| collection_id | net_id |
|---|---|
| 10 | herrera1988 |
| 10 | Burkle2013 |
| 10 | bartomeus2008 |
| 10 | Olito-Fox2014 |
| 10 | Benadi2013_4(1700m)+Benadi2013_5(1800m) |
| 10 | Baldock2011_TB+Baldock2011_JN |
| 10 | Chamberlain_HLU+Chamberlain_HLG+Chamberlain_OKU+Chamberlain_OKG+Chamberlain_WLU+Chamberlain_WLG+Chamberlain_SOU+Chamberlain_SOG |
| 10 | Chamberlain_Site1+Chamberlain_Site2+Chamberlain_Site3+Chamberlain_Site4+Chamberlain_Site5+Chamberlain_Site6 |
| 10 | Devoto2005_LQ |
| 10 | Devoto2005_LT+Devoto2005_LH |
| 10 | Devoto2005_LL+Devoto2005_CT |
| 10 | Dupont2009_IsenBjerg+Dupont2009_Other |
| 10 | Gibson2006_GA1 |
| 10 | LaraRomero2016_pe?alara_EP+LaraRomero2016_pe?alara_PA+LaraRomero2016_nevero_EP+LaraRomero2016_nevero_PA |
| 10 | Marrero2013 |
| 10 | Trojelsgaard2015_Tenerife Teno Bajo+Trojelsgaard2015_Tenerife Fasnia |
| 10 | Vanbergen2013_balfarm+Vanbergen2013_bridgend+Vanbergen2013_dalhaikie+Vanbergen2013_netherton+Vanbergen2013_backhill+Vanbergen2013_corntulloch+Vanbergen2013_allancreich |
| 10 | Fragoso_RA2+Fragoso_RA3+Fragoso_RD1+Fragoso_RD3 |
| 10 | Pornon2017 |
| 10 | Orford_B6+Orford_B7+Orford_B8+Orford_B9 |
| 10 | Blumel2016 |
| 10 | Kantsa2018 |
| 10 | Grass2013_1+Grass2013_2+Grass2013_3+Grass2013_4+Grass2013_5+Grass2013_6+Grass2013_7+Grass2013_8+Grass2013_9+Grass2013_10+Grass2013_11+Grass2013_12+Grass2013_13+Grass2013_14+Grass2013_15+Grass2013_16+Grass2013_17 |
| 10 | CordenizPicanco2018_NatVeg |
| 10 | Hackett2019_UK_sand_dune+Hackett2019_UK_grassland+Hackett2019_UK_heathland+Hackett2019_UK_woodland+Hackett2019_UK_salt_marsh+Hackett2019_UK_scrub |
| 10 | Traveset2013_Pinta |
| 10 | Traveset2013_SanCristobal |
| 10 | Simanonok2014 |
| 10 | Baldock2019_Edinburgh |
| collection_id | net_id |
|---|---|
| 11 | kato1990 |
| 11 | ramirez1989 |
| 11 | Kato1993 |
| collection_id | net_id |
|---|---|
| 12 | Chamberlain_cr1+Chamberlain_cr2+Chamberlain_fs1+Chamberlain_fs2+Chamberlain_go1+Chamberlain_go2+Chamberlain_mm1+Chamberlain_mm2+Chamberlain_mz1+Chamberlain_mz2+Chamberlain_sm1+Chamberlain_sm2 |
| 12 | Dattilo2016 |
| 12 | KatoMiura1996 |
| collection_id | net_id |
|---|---|
| 13 | olensen2002aig |
| collection_id | net_id |
|---|---|
| 14 | Trojelsgaard2015_El Hierro |
| collection_id | net_id |
|---|---|
| 15 | Gibson2006_GA2 |
Une fois le modèle de collection appliqué nous obtenons les structures suivantes:
##
## Pour la collection 1 du modèle *pirho*
## [1] "arroyo1982_1+arroyo1982_2+arroyo3"
## [2] "dupont2003"
## [3] "petanidou1991"
## [4] "Aizen2008_Challhuaco_U+Aizen2008_Challhuaco_D"
## [5] "Aizen2008_Llao-llao_U+Aizen2008_Llao-llao_D"
## [6] "Jedrzejewska2013_Ochata+Jedrzejewska2013_Kabaty"
## [7] "Pinheiro2008"
## [8] "Souza_pantanal"
## [9] "Robinson2018"
## [10] "Jolls2019"
## [11] "Traveset2013_Fernandina"
## [12] "Baldock2019_Leeds"
## [13] "Baldock2019_Reading"
##
## Pour la collection 2 du modèle *pirho*
## [1] "Benadi2013_3(1340m)" "Trojelsgaard2015_La Gomera"
## [3] "CordenizPicanco2018_SemiPast"
##
## Pour la collection 3 du modèle *pirho*
## [1] "Kato2000" "Freitas2006" "Inoue1990"
## [4] "Souza_cerrado" "Adedoja2019" "Baldock2019_Bristol"
##
## Pour la collection 4 du modèle *pirho*
## [1] "Aizen2008_Puerto Blest_U+Aizen2008_Puerto Blest_D"
## [2] "LemusJimenez2003"
##
## Pour la collection 5 du modèle *pirho*
## [1] "inouye1988"
## [2] "Junker2013"
## [3] "Kehinde2014_Joostenberg_Conv+Kehinde2014_Joostenberg_Org+Kehinde2014_Joostenberg_Nat+Kehinde2014_Laibach_Conv+Kehinde2014_Laibach_Org+Kehinde2014_Laibach_Nat+Kehinde2014_Spier_Conv+Kehinde2014_Spier_Nat"
## [4] "Watts2016_Chicon+Watts2016_Mantanay+Watts2016_Choquebamba+Watts2016_Huaran+Watts2016_Piscacucho+Watts2016_Poques+Watts2016_Pumamarca+Watts2016_Tiaparo+Watts2016_Yanacocha"
## [5] "Kakutani1990"
## [6] "Fragoso_RA1+Fragoso_RD2"
## [7] "Souza_chaco"
## [8] "Oleques2019"
##
## Pour la collection 6 du modèle *pirho*
## [1] "medan2002ld"
## [2] "small1976"
## [3] "smith-ramirez2005"
## [4] "Benadi2013_1(950m)+Benadi2013_2(1170m)+Benadi2013_6(2020m)"
## [5] "Shay2016"
## [6] "Aizen2008_Cerro Otto_U+Aizen2008_Cerro Otto_D"
## [7] "Lundgren2005"
## [8] "Zackenberg"
## [9] "Carstensen_Gigante+Carstensen_Paulino+Carstensen_Tinkerbell+Carstensen_Midway+Carstensen_Cedro+Carstensen_Elefante+Carstensen_Soizig"
## [10] "Welti_ID+Welti_K1B+Welti_K4A+Welti_4B+Welti_20B+Welti_20C+Welti_N1A+Welti_N1B+Welti_N4A+Welti_N4B+Welti_N20A+Welti_N20B"
## [11] "Bennett2018"
## [12] "CordenizPicanco2018_NatFor"
## [13] "CordenizPicanco2018_ExoFor"
## [14] "CordenizPicanco2018_IntPast"
## [15] "Benadi2018"
## [16] "Villalobos2019"
## [17] "Traveset2013_Santiago"
## [18] "Traveset2013_SantaCruz"
## [19] "Son2019_a1+Son2019_a2+Son2019_a3+Son2019_a4+Son2019_a5+Son2019_a6+Son2019_a7+Son2019_a8+Son2019_F1+Son2019_F2+Son2019_F3+Son2019_F4+Son2019_F5+Son2019_F6+Son2019_F7+Son2019_F8"
## [20] "Sritongchuay2019_near+Sritongchuay2019_far"
##
## Pour la collection 7 du modèle *pirho*
## [1] "medan2002rb"
## [2] "olensen2002flo"
## [3] "vazquez2002"
## [4] "Trojelsgaard2015_Gran Canaria"
## [5] "Trojelsgaard2015_Western Sahara"
## [6] "LaraRomero2019_blanca+LaraRomero2019_rajada+LaraRomero2019_refugio+LaraRomero2019_torre"
##
## Pour la collection 8 du modèle *pirho*
## [1] "Weiner2011"
## [2] "Kaiser_control+Kaiser_restored"
## [3] "Gilarranz2014_amarante+Gilarranz2014_barrosa+Gilarranz2014_cincocerros+Gilarranz2014_difuntito+Gilarranz2014_difuntos+Gilarranz2014_elmorro+Gilarranz2014_labrava+Gilarranz2014_lachata+Gilarranz2014_lapaja+Gilarranz2014_piedraalta+Gilarranz2014_vigilancia+Gilarranz2014_volcan"
## [4] "Kaiser-Bunbury2017_Bernica+Kaiser-Bunbury2017_Casse-dent+Kaiser-Bunbury2017_Copolia+Kaiser-Bunbury2017_La-Reserve+Kaiser-Bunbury2017_Rosebelle+Kaiser-Bunbury2017_Salazie+Kaiser-Bunbury2017_Tea-Plantation+Kaiser-Bunbury2017_Trois-Freres"
## [5] "Fang2012"
## [6] "Gibson2006_SG"
## [7] "Gibson2006_TA1"
## [8] "Trojelsgaard2015_Fuerteventura"
## [9] "Pfeiffer_CNE+Pfeiffer_CNM+Pfeiffer_CNT+Pfeiffer_CPB+Pfeiffer_CPM+Pfeiffer_CPR+Pfeiffer_CPS+Pfeiffer_M2+Pfeiffer_RP1+Pfeiffer_RP2+Pfeiffer_LM+Pfeiffer_LO+Pfeiffer_BD+Pfeiffer_BH+Pfeiffer_BS"
## [10] "Biella2019"
## [11] "Nel2017"
## [12] "Ferrero2013"
## [13] "Neli2014"
##
## Pour la collection 9 du modèle *pirho*
## [1] "eberling1999"
## [2] "ramirez1992"
## [3] "Struck1994"
## [4] "Albrecht2010_49yr+Albrecht2010_63yr+Albrecht2010_84yr+Albrecht2010_109yr+Albrecht2010_130yr"
## [5] "Devoto2005_PP+Devoto2005_AP"
## [6] "Devoto2005_VT"
## [7] "Gibson2006_TA2"
## [8] "MonteroCastano2017_Albufera+MonteroCastano2017_Llimpa+MonteroCastano2017_Tirant"
## [9] "Yoshihara2008"
## [10] "PopicThesis"
## [11] "Orford_B1+Orford_B2+Orford_B3+Orford_B4+Orford_B5+Orford_B10"
## [12] "Souza_vereda"
## [13] "Adedoja2018b_baseZone+Adedoja2018b_MidZone+Adedoja2018b_HighZone+Adedoja2018b_PeakZone"
## [14] "Hackett2019_NZ_salt_marsh+Hackett2019_NZ_sand_dune+Hackett2019_NZ_scrub_coprosma"
##
## Pour la collection 10 du modèle *pirho*
## [1] "herrera1988"
## [2] "Burkle2013"
## [3] "bartomeus2008"
## [4] "Olito-Fox2014"
## [5] "Benadi2013_4(1700m)+Benadi2013_5(1800m)"
## [6] "Baldock2011_TB+Baldock2011_JN"
## [7] "Chamberlain_HLU+Chamberlain_HLG+Chamberlain_OKU+Chamberlain_OKG+Chamberlain_WLU+Chamberlain_WLG+Chamberlain_SOU+Chamberlain_SOG"
## [8] "Chamberlain_Site1+Chamberlain_Site2+Chamberlain_Site3+Chamberlain_Site4+Chamberlain_Site5+Chamberlain_Site6"
## [9] "Devoto2005_LQ"
## [10] "Devoto2005_LT+Devoto2005_LH"
## [11] "Devoto2005_LL+Devoto2005_CT"
## [12] "Dupont2009_IsenBjerg+Dupont2009_Other"
## [13] "Gibson2006_GA1"
## [14] "LaraRomero2016_pe?alara_EP+LaraRomero2016_pe?alara_PA+LaraRomero2016_nevero_EP+LaraRomero2016_nevero_PA"
## [15] "Marrero2013"
## [16] "Trojelsgaard2015_Tenerife Teno Bajo+Trojelsgaard2015_Tenerife Fasnia"
## [17] "Vanbergen2013_balfarm+Vanbergen2013_bridgend+Vanbergen2013_dalhaikie+Vanbergen2013_netherton+Vanbergen2013_backhill+Vanbergen2013_corntulloch+Vanbergen2013_allancreich"
## [18] "Fragoso_RA2+Fragoso_RA3+Fragoso_RD1+Fragoso_RD3"
## [19] "Pornon2017"
## [20] "Orford_B6+Orford_B7+Orford_B8+Orford_B9"
## [21] "Blumel2016"
## [22] "Kantsa2018"
## [23] "Grass2013_1+Grass2013_2+Grass2013_3+Grass2013_4+Grass2013_5+Grass2013_6+Grass2013_7+Grass2013_8+Grass2013_9+Grass2013_10+Grass2013_11+Grass2013_12+Grass2013_13+Grass2013_14+Grass2013_15+Grass2013_16+Grass2013_17"
## [24] "CordenizPicanco2018_NatVeg"
## [25] "Hackett2019_UK_sand_dune+Hackett2019_UK_grassland+Hackett2019_UK_heathland+Hackett2019_UK_woodland+Hackett2019_UK_salt_marsh+Hackett2019_UK_scrub"
## [26] "Traveset2013_Pinta"
## [27] "Traveset2013_SanCristobal"
## [28] "Simanonok2014"
## [29] "Baldock2019_Edinburgh"
##
## Pour la collection 11 du modèle *pirho*
## [1] "kato1990" "ramirez1989" "Kato1993"
##
## Pour la collection 12 du modèle *pirho*
## [1] "Chamberlain_cr1+Chamberlain_cr2+Chamberlain_fs1+Chamberlain_fs2+Chamberlain_go1+Chamberlain_go2+Chamberlain_mm1+Chamberlain_mm2+Chamberlain_mz1+Chamberlain_mz2+Chamberlain_sm1+Chamberlain_sm2"
## [2] "Dattilo2016"
## [3] "KatoMiura1996"
##
## Pour la collection 13 du modèle *pirho*
## [1] "olensen2002aig"
##
## Pour la collection 14 du modèle *pirho*
## [1] "Trojelsgaard2015_El Hierro"
##
## Pour la collection 15 du modèle *pirho*
## [1] "Gibson2006_GA2"Et voici donc les valeurs numériques pour les \(\alpha\) (paramètres de connectivité).
Pour la collection 1 : \[\begin{bmatrix} 0.52 &0.6 &0.34 &0.1 &0.15 &0 &0.36 \\0.12 &0.93 &0.01 &0.01 &0 &0.61 &0.16 \\0.05 &0.31 &0.02 &0.08 &0.37 &0.27 &0.12 \\0.04 &0.05 &0.01 &0.38 &0.03 &0.01 &0.17 \\0 &0.03 &0.16 &0.11 &0.04 &0.01 &0.01 \\0.01 &0.22 &0.02 &0.01 &0.05 &0 &0.01 \\ \end{bmatrix}\] Pour la collection 2 : \[\begin{bmatrix} 0.66 &0.23 \\0.2 &0.05 \\ \end{bmatrix}\] Pour la collection 3 : \[\begin{bmatrix} 0.64 &0.32 &0.11 &0.53 &0.19 &0.05 \\0.47 &0.21 &0.02 &0.19 &0.07 &0.03 \\0.16 &0.05 &0.01 &0.07 &0.01 &0 \\ \end{bmatrix}\] Pour la collection 4 : \[\begin{bmatrix} 0.45 &0.07 \\0.22 &0.62 \\0.23 &0.04 \\ \end{bmatrix}\] Pour la collection 5 : \[\begin{bmatrix} 0.78 &0.43 &0.16 &0.56 \\0.29 &0.04 &0.22 &0.08 \\0.02 &0.12 &0.03 &0 \\ \end{bmatrix}\] Pour la collection 6 : \[\begin{bmatrix} 0.82 &0.63 &0.2 &0.74 \\0.34 &0.07 &0.41 &0.13 \\0.02 &0.16 &0.03 &0 \\ \end{bmatrix}\] Pour la collection 7 : \[\begin{bmatrix} 0.9 &0.46 &0.72 \\0.17 &0.37 &0.03 \\ \end{bmatrix}\] Pour la collection 8 : \[\begin{bmatrix} 0.66 &0.97 &0.72 &1 &0.13 &0.71 &0 \\0.99 &0.93 &0.84 &0.64 &0.5 &0.11 &0.17 \\0.71 &0.7 &0.28 &0.32 &0.13 &0.07 &0.05 \\0.96 &0.46 &0.75 &0.14 &0.39 &0.01 &0.07 \\0.62 &0.36 &0.09 &0.11 &0.04 &0.02 &0.01 \\0.62 &0.12 &0.43 &0.02 &0.17 &0 &0.02 \\0.33 &0.03 &0.14 &0 &0.03 &0 &0 \\ \end{bmatrix}\] Pour la collection 9 : \[\begin{bmatrix} 0.59 &0.17 &0.32 \\0.06 &0.15 &0.02 \\ \end{bmatrix}\] Pour la collection 10 : \[\begin{bmatrix} 0.91 &0.62 &0.3 &0.79 &0.44 \\0.15 &0.7 &0.32 &0.07 &0.36 \\0.15 &0.03 &0.16 &0.05 &0.01 \\ \end{bmatrix}\] Pour la collection 11 : \[\begin{bmatrix} 0.09 &0.36 &1 &0.12 &0.41 \\0.33 &0 &0.07 &0.46 &0.09 \\0 &0.01 &0.07 &0.14 &0 \\0.03 &0.16 &0.02 &0 &0 \\ \end{bmatrix}\] Pour la collection 12 : \[\begin{bmatrix} 0.68 &0.37 &0.12 \\0.41 &0.17 &0.04 \\0.19 &0.05 &0.01 \\ \end{bmatrix}\] Pour la collection 13 : \[\begin{bmatrix} 0.78 \\0.19 \\ \end{bmatrix}\] Pour la collection 14 : \[\begin{bmatrix} 0.44 &0.08 \\ \end{bmatrix}\] Pour la collection 15 : \[\begin{bmatrix} 0.42 &1 \\0.35 &0.01 \\ \end{bmatrix}\]
Répartition dans les clusters selon la taxonomie
## `summarise()` has grouped output by 'col_id', 'taxo'. You can override using
## the `.groups` argument.
## `summarise()` has grouped output by 'col_id', 'taxo'. You can override using
## the `.groups` argument.
Pollinators repartition for the pirho model regarding taxonomy
## Warning: Removed 24 rows containing missing values (`geom_bar()`).
Pollinators repartition for the pirho model regarding taxonomy
Plants repartition for the pirho model regarding taxonomy
## Warning: Removed 238 rows containing missing values (`geom_bar()`).
Plants repartition for the pirho model regarding taxonomy